force unbuffered output for the console
Figure out the problem. The python interpreter can be forced to use unbuffered prints if we set the PYTHONUNBUFFERED environment variable. Just use
export PYTHONUNBUFFERED=on
Nevertheless that still did not solved completely my problem because I had a piped  grep together with blender. Hence, although blender was running unbuffered outputs to console, grep was... Just used grep --line-buffered (saw that in s very good post about stdout here https://eklitzke.org/stdout-buffering)
Hope that helps somebody! Thanks for everyone that tried to help!
/edit:
Since 16.01.2020, to make this work you have to launch blender with --python-use-system-env to make it work.
Source: https://developer.blender.org/rBS7c2f0074f3fe2411daa7a6e351d7cbc535246871